Are these people clinically insane? They want to genetically modify coffee without caffeine biosynthesis pathways? If anything they should be working on the modification of the caffeine synthetase expression promoters for the up regulation of the pathway. No more quadruple espressos to keep you going during a late night hacking session, one shot should be enough if the caffeine content was 10X normal, think natural jolt coffee.
On second thought: The idea of sticking the caffeine gene in the human genome proposed earlier is not so unbelievable (except for the small ethical/technical matter of germ line therapy, which I will leave well alone ;-). Caffeine in coffee and tea is synthesised from purines with a few methylation steps along the way, not uncommon stuff in human anabolic pathways. However it would be
a good idea to set-up an automatic expression control system, so when your brain starts releasing sleep inducing peptides, such as GHRH, at some inconvenient hour of the morning, these same sleep peptides could activate some transcription factor (TF) that bumps up expression of the caffeine synthetase enzyme (and associated pathway enzymes) in a big way, meanwhile you could remove the caffeine gene from coffee and swap it for some chemical that inhibits the caffeine up regulating TF, that way you're default setting is alertness and you'd drink coffee to get to sleep.
I'd do the same kind of thing with THC, only in this case THC will get up regulated by some drug no one will ever illegalise like aspirin, so popping standard painkillers would get you stoned...